The latest developments in industry involved the deployment of digital twins for both long and short term decision making, such as supply chain management, production planning and control. Modern production environments are frequently subject to disruptions and consequent modifications. As a result, the development of digital twins of manufacturing systems cannot rely solely on manual operations. Recent contributions proposed approaches to exploit data for the automated generation of the models. However, the resulting representations can be excessively accurate and may also describe activities that are not significant for estimating the system performance. Generating models with an appropriate level of detail can avoid useless efforts and long computation times, while allowing for easier understanding and re-usability. This paper proposes a method to automatically discover manufacturing systems and generate adequate digital twins. The relevant characteristics of a production system are automatically retrieved from data logs. The proposed method has been applied on two test cases and a real manufacturing line. The experimental results prove its effectiveness in generating digital models that can correctly estimate the system performance.